CLDN19 p.Pro215=
c.645C>T · rs777425105 · VCV795078
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.123%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2 | GERP -3.2 |
| Overall | ||
| CADD | 7.021 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.123%
East Asian · 55/44,882 alleles
Filtering AF
0.0967%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0873%
Overall
0.00483%
78/1,614,010 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.123% | 816 |
| African / African-American | 0.00799% | 12,509 |
| European (non-Finnish) | 0.00136% | 73,744 |
| South Asian | 0.0011% | 91,056 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CLDN19
- Protein
- p.Pro215=
- Coding
- c.645C>T
- MANE Select
- NM_148960
- dbSNP
- rs777425105
- Type
- single nucleotide variant
- Location
- chr1:42735116 (GRCh38)
- Gene constraint
- LOEUF 1.254 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.08
- Residue 215
- the 'disordered' region
Similar variants
- CLDN19 p.Gly20Asp Pathogenic/Likely pathogenic ★★ same type
- CLDN19 p.Gly75Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- CLDN19 p.Leu90Arg Pathogenic/Likely pathogenic ★★ same type
- CLDN19 p.Pro28Leu Likely pathogenic ★★ same type
- CLDN19 c.-150C>T Uncertain significance ★★ same type
- CLDN19 p.Ala216Thr Uncertain significance ★★ ⚠ same type
- CLDN19 p.Ala218Thr Uncertain significance ★★ ⚠ same type
- CLDN19 p.Ala55Thr Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/cldn19-p-pro215 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown